So many (stale?) flavors reused from TOS, starting with the obsessed scientist (Daystrom, The Ultimate Computer) with a touch of misguided rank-puller (Fox, A Taste of Armageddon; Ferris, The Galileo Seven). The misbehaving computer (Tomorrow is Yesterday, Court Martial, The Menagerie). The scientific probe launch (The Immunity Syndrome). The dilemma of whether to kill a sentient but dangerous lifeform (The Man Trap). Alien life inhabiting and speaking through a crew member (The Lights of Zetar, Return to Tomorrow) (and a GREAT job as always from Spiner). And the provision of a bare planet as a new home for the now-subdued enemy (Space Seed).
I also caught a flavor of http://en.wikipedia.org/wiki/Fantastic_Voyage in the miniaturization aspect, as well as The Andromeda Strain in the escaped-from-lab aspect.
Then there are all the "let the viewer identify" elements, most obvious in TOS as Earth-copied alien planets and problems and time travel back to Earth (City on the Edge of Forever, Tomorrow is Yesterday). Here we have regular natural phenomenon ("just like geysers", gosh), everything Wesley (mother-son issues, teenage issues, school-project/all-nighter issues, admitting-mistakes issues), prodigy/fame issues, and of all things baseball obsession (what?).
As to "Evolution", obviously it is referring to the evolution of the Nanites into a collective sentience, but also of course to Stubbs's psychological evolution away from narrow obsession into compassionate humility, aided by Troi of course and also by the Nanites' near success in killing him and the doctor's success in saving him. This at least is different from TOS, where the misguided always got poetic justice at the end. Finally must be mentioned Wesley's supposed social evolution, but it's really just a tag line joke, blechh.
Best part of the episode: Wesley's 'fessing up to Mom followed by Mom doing the crew briefing. Wheaton gets to show his chops, such as they are, and Mom steps up to run interference for her son. Only problem is why didn't Wesley, as the expert, have more to say as to Nanite details at that point; I suppose we can chalk that up to them having evolved already beyond his expertise...